Hierarchical cluster analysis as a tool to manage variation in germplasm collections

Summary The potential of using hierarchical cluster analysis to classify entries from a germplasm collection according to their degree of similarity was assessed. Results suggest that similarity is generally greatest among individual entries by country of origin and that hierarchical cluster analysis could be used as a tool to classify entries from germplasm collections according to their respective gene pools, even when no passport data are available. Based on this technique, it is also shown that the segregative potential of entries can be estimated.     

Historical Museology Meets Tropical Biodiversity Conservation

The great scientific importance of historical collections is a well-established fact. On the contrary, their value as vehicles to promote public awareness and effective conservation projects in some of the most valuable biodiversity hotspots in the tropics appear to have been greatly overlooked by Natural History Museums and similar institutions. Utilising the vertebrate collections of Italian institutions as a case study, the great potential of these medium-sized museums to popularising and promoting biodiversity in some of the most valuable regions of the world, utilising the history of their collections and of the men which collected and studied them, is emphasised.     

The convention on Biological Diversity: Some implications for microbiology and microbial culture collections

The coming into force of the Convention on Biological Diversity has led to a series of discussions aiming to clarify its implementation. A number of uncertainties exist at the microbial level and there is a lack of awareness of the role played by microorganisms in ecosystem function. There is moreover a great lack of knowledge about the number of species of microorganisms that exist, their distribution, stability in the environment and intricate interactive roles. Conservation and use of biological material for sustainable environmental management are major issues. Specialist microbiological input into the debate is required to ensure that provisions made for national programmes are appropriate and practicable at the microbiological level. The Articles of the Convention of special relevance to microbiologists are listed and discussed. The role of microbial culture collections within the framework of the Convention is considered. The difficulties and uncertainties of conservation and study of microorganisms in their habitat (in situ) increase the need forex situ conservation in microbial culture collections. The World Federation for Culture Collections plays a coordinating role with regard to expertise, information, training and the management and operation of microbial resource centres. It has the potential for providing a special interest Clearing House Mechanism for the support of the Convention.     

DNA BARCODING OF CHLORARACHNIOPHYTES USING NUCLEOMORPH ITS SEQUENCES1

Chlorarachniophytes are a small group of marine photosynthetic protists. They are best known as examples of an intermediate stage of secondary endosymbiosis: their plastids are derived from green algae and retain a highly reduced nucleus, called a nucleomorph, between the inner and outer pairs of membranes. Chlorarachniophytes can be challenging to identify to the species level, due to their small size, complex life cycles, and the fact that even genus‐level diagnostic morphological characters are observable only by EM. Few species have been formally described, and many available culture collection strains remain unnamed. To alleviate this difficulty, we have developed a barcoding system for rapid and accurate identification of chlorarachniophyte species in culture, based on the internal transcribed spacer (ITS) region of the nucleomorph rRNA cistron. Although this is a multicopy locus, encoded in both subtelomeric regions of each chromosome, interlocus variability is low due to gene conversion by homologous recombination in this region. Here, we present barcode sequences for 39 cultured strains of chlorarachniophytes (>80% of currently available strains). Based on barcode data, other published molecular data, and information from culture records, we were able to recommend names for 21 out of the 24 unidentified, partially identified, or misidentified chlorarachniophyte strains in culture. Most strains could be assigned to previously described species, but at least two to as many as five new species may be present among cultured strains.     

The rediscovery of part of the Ceres Hispanica collection of M. Lagasca and S. R. Clemente

Thirty sheets of Gramineae, recently found in the Real Colegio Alfonso XII of San Lorenzo de El Escorial, belong to Lagasca & Clemente's Ceres Hispanica herbarium. The main corpus of the Ceres Hispanica collection is kept in the Real Jardín Botánico de Madrid, and the missing sheets were reported as having disappeared in 1823. The importance of the rediscovered material is evaluated from the point of view of its historical relevance.     

Notes on an important botanical trip (1799–1800) of J. P. Rottler on the Goromandel Coast (India) with a translation of his original text, explanatory notes and a map

MATTHEW, KM., 1993. Notes on an important botanical trip (1799–1800) of J. P. Rottler on the Coromandel Coast (India) with a translation of his original text, explanatory notes and a map . J. P. Rottler (1749–1836) made extensive collections on the Coromandel Coast in south India. The paper presented here in translation was one of Rottler's major publications, which, along with four indexes and a map, now newly prepared, should prove useful for a new study of Rottler's contributions.     

Fluid‐preserved fishes are one solution for assessing historical change in fish trophic level

1. There are few resources available for assessing historical change in fish trophic dynamics, but specimens held in natural history collections could serve as this resource. In contemporary trophic ecology studies, trophic and source information can be obtained from compound‐specific stable isotope analysis of amino acids of nitrogen (CSIA‐AA‐N).
2. We subjected whole Sebastes ruberrimus and Clupea pallasii to formalin fixation and 70% ethanol preservation. We extracted tissue samples from each fish pre‐fixation, after each chemical change, and then in doubling time for 32–64 days once placed in the final preservative. All samples were subjected to CSIA‐AA‐N, and their glutamic acid and phenylalanine profiles and associated trophic position were examined for differences over time by species.
3. Glutamic acid and phenylalanine values were inconsistent in direction and magnitude, particularly during formalin fixation, but stabilized similarly (in 70% ethanol) among conspecifics. In some cases, the amino acid values of our final samples were significantly different than our initial pre‐preservation samples. Nonetheless, significant differences in glutamic acid, phenylalanine, and estimated trophic position were not detected among samples that were in 70% ethanol for >24 hr.
4. Our results suggest that the relative trophic position of fluid‐preserved specimens can be estimated using CSIA‐AA‐N, and CSIA‐AA‐N estimates for fluid‐preserved specimens should only be reported as relative differences. Timelines of trophic position change can be developed by comparing specimens collected at different points in time, revealing trophic information of the past and cryptic ecosystem responses.

     

Enthesopathies as occupational stress markers: Evidence from the upper limb

Enthesopathies—that is, “musculo‐skeletal stress markers”—are frequently used to reconstruct past lifestyles and activity patterns. Relatively little attention has been paid in physical anthropology to methodological gaps implicit in this approach: almost all methods previously employed neglect current medical insights into enthesopathies and the distinction between healthy and pathological aspects has been arbitrary. This study presents a new visual method of studying fibrocartilaginous enthesopathies of the upper limb (modified from Villotte: Bull Mém Soc Anthropol Paris n.s. 18 (2006) 65–85), and application of this method to 367 males who died between the 18th and 20th centuries, from four European identified skeletal collections: the Christ Church Spitalfields Collection, the identified skeletal collection of the anthropological museum of the University of Coimbra, and the Sassari and Bologna collections of the museum of Anthropology, University of Bologna. The analysis, using generalized estimating equations to model repeated binary outcome variables, has established a strong link between enthesopathies and physical activity: men with occupations involving heavy manual tasks have significantly (P‐value < 0.001) more lesions of the upper limbs than nonmanual and light manual workers. Probability of the presence of an enthesopathy also increases with age and is higher for the right side compared with the left. Our study failed to distinguish significant differences between the collections when adjusted for the other effects. It appears that enthesopathies can be used to reconstruct past lifestyles of populations if physical anthropologists: 1) pay attention to the choice of entheses in their studies and 2) use appropriate methods. Am J Phys Anthropol, 2010. © 2009 Wiley‐Liss, Inc.     

Strengths and weaknesses of museum and national survey data sets for predicting regional species richness: comparative and combined approaches

We compiled three independent data sets of bird species occurrences in northeastern Colorado to test how predicted species richness compared to a combined analysis using all the data. The first data set was a georeferenced regional museum data set from two major repositories — the Denver Museum of Nature, and the Science and University of Colorado Museum. The two national survey data sets were the Breeding Bird Survey (summer), and the Great Backyard Bird Count (winter). Resulting analyses show that the museum data sets give richness estimates closest to the combined data set while exhibiting a skewed abundance distribution, whereas survey data sets do not accurately estimate overall richness even though they contain far more records. The combined data set allows the strengths of one data set to augment weaknesses in others. It is likely some museum data sets display skewed abundance distributions due to collectors’ potentially self‐selecting under‐represented species over common ones.